Force causes acceleration. If the force is time varying, so will be the acceleration. If you want to calculate the instantaneous force, you use the instantaneous acceleration, but if you only need the time averaged force, you can use the average acceleration.

As said above, it depends which force you want. if you use the change of acceleration, you get the change of force. If you use accerlation at time X, you get force at time X. I always wondered why they never taught that in my physics class (that your bringing more than just variables with your equations).